Variant report

Variant	rs1840846
Chromosome Location	chr5:58604766-58604767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1031197	0.81[ASN][1000 genomes]
rs10491352	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10940644	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11959132	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12189022	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519611	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12521263	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12522944	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1445952	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1445953	0.90[EUR][1000 genomes]
rs1445954	0.91[EUR][1000 genomes]
rs1579848	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1579849	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16889479	0.90[EUR][1000 genomes]
rs16889499	0.91[EUR][1000 genomes]
rs16889518	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17444185	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17528522	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17528578	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17780175	0.81[ASN][1000 genomes]
rs1823070	0.91[EUR][1000 genomes]
rs1867711	0.91[EUR][1000 genomes]
rs1867712	0.91[EUR][1000 genomes]
rs1947090	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1947095	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2013979	0.83[ASN][1000 genomes]
rs2014012	0.83[ASN][1000 genomes]
rs2028836	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4700328	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6877508	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs889231	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58593000-58611200	Weak transcription	Right Ventricle	heart
2	chr5:58593200-58612600	Weak transcription	Fetal Lung	lung
3	chr5:58593200-58613400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:58593800-58604800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:58594000-58612800	Weak transcription	Stomach Mucosa	stomach
6	chr5:58594400-58606000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:58595600-58609000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:58597000-58607600	Weak transcription	Psoas Muscle	Psoas
9	chr5:58598000-58607800	Weak transcription	Fetal Heart	heart
10	chr5:58598000-58608600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:58598000-58612600	Weak transcription	Fetal Intestine Large	intestine
12	chr5:58598000-58612800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:58598000-58612800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:58600400-58604800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:58602400-58606600	Weak transcription	Hela-S3	cervix
16	chr5:58604400-58604800	Strong transcription	A549	lung
17	chr5:58604400-58605000	ZNF genes & repeats	Fetal Stomach	stomach
18	chr5:58604400-58606000	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr5:58604600-58604800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr5:58604600-58605000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:58604600-58605000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:58604600-58605000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:58604600-58605000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:58604600-58605000	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr5:58604600-58605200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:58604600-58605200	ZNF genes & repeats	Fetal Brain Female	brain
27	chr5:58604600-58605600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr5:58604600-58605800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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